2-DE	Two-dimensional gel electrophoresis
AI	Artificial Intelligence
AML	Acute myeloid leukemia
APOAII	Apolipoprotein-AII
APOLLO	Applied Proteogenomics Organizational Learning and Outcomes
ART	Antibiotic resistance
AS	Alternative splicing
AST	Antibiotic susceptibility testing
CAF	Cancer-associated fibroblasts
CASK	Calcium/calmodulin-dependent serine protein kinase
CCA	Cholangiocarcinoma
CD	Crohn’s disease
CDI	Clostridium difficile infection
CEMIP	Cell migration-inducing and hyaluronan-binding protein
CHAT	Cancer Hallmarks Analytics Tool
CPTAC	Clinical Proteomic Tumor Analysis Consortium
CRC	Colorectal cancer
DAVID	The Database for Annotation, Visualization and Integrated Discovery
DDA	Data dependent analysis
DIA	Data independent analysis
DMS	Differential ion mobility MS
EDRN	Early Detection Research Network
EV	Extracellular vesicles
FASN	Fatty acid synthase
FFPE	Formalin-fixed paraffin-embedded
FMT	Fecal microbiota transplantation
Fn	Fusobacterium nucleatum
GELFREE	Gel-eluted liquid fractionation entrapment electrophoresis
HCC	Hepatocellular carcinoma
HGSC	High-grade serous ovarian carcinoma
HoC	Hallmarks of Cancer
hPOP	Human Personal Omics Profiling
HPP	Human Proteomics Project
HPRL	Proteome Reference Library
hTERT	Human telomerase reverse transcriptase
HUPO	Human Protein Organisation
IARC	International Agency for Research on Cancer
IBD	Inflammatory bowel disease
ICP	Inductively coupled argon plasma
ICPC	International Cancer Proteogenome Consortium
IHC	Immunohistochemistry
IPA	Ingenuity pathway analysis
iTRAQ	Isobaric tagging for multiplexed relative and absolute protein quantitation
LOXL-4	Lysyl oxidase-like 4
LPS	Lipopolysaccharide
LRG	Leucine-rich α-2 glycoprotein
LUAD	Lung adenocarcinoma
MAT2A	Methionine adenosyltransferase 2a
mdCAT	Mass-defect-based carbonyl activated tag
MDD	Major depressive disorder
MRM	Multiple reaction monitoring
MudPIT	Multidimensional protein identification technology
NNMT	Nicotinamide N-methyltransferase
NSCLC	Non-small cell lung cancer
NTME	Nontumor microenvironment
OS	Overall survival
PCT	Pressure cycling technology
PDAC	Pancreatic ductal adenocarcinoma
PHOENIX	The Chinese Pilot Hub Of Encyclopedic Proteomix
PPTT	Plasmonic photothermal therapy
PRM	Parallel reaction monitoring
PTMs	Posttranslational modifications
QSOX1	Quiescin sulfhydryl oxidase 1
QTOF	Quadrupole time-of-flight
RA	Rheumatoid arthritis
RBFOX3	RNA binding protein fox-1 homolog 3
ROS	Reactive oxygen species
RPMAs	Reverse phase microarrays
RPPA	Reverse-phase protein microarray
RFS	Recurrence-free survival
SAPs	Single amino acid polymorphisms
SCFAs	short-chain fatty acids
SDS-PAGE	Sodium dodecyl sulfate polyacrylamide gel electrophoresis
SERS	Surface-enhanced Raman scattering
SILAC	Stable isotope labeling by/with amino acids in cell culture
SRM	Selective reaction monitoring
suPAR	Soluble urokinase-type plasminogen activator receptor
SWATH-MS	Sequential window acquisition of all theoretical mass spectra
TCGA	The Cancer Genome Atlas
TME	Tumor microenvironment
TMT	Tandem mass tag
TNBC	Triple negative breast cancer
TOTT	The Oncology Think Tank
uPAR	Urokinase plasminogen activator receptor